Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol
The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Bile samples will be collected in endoscopic retrograde cholangi...
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| Published in: | PloS one Vol. 15; no. 11; p. e0242553 |
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| Format: | Journal Article |
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19-11-2020
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| Abstract | The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases.
Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes.
The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.
NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426. |
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| AbstractList | Background The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Methods Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes. Results The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases. Trial registration NCT04391426. Registered 18 May 2020, BackgroundThe performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases.MethodsBile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes.ResultsThe primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.Trial registrationNCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426. Background The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Methods Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes. Results The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases. Trial registration NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426. The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes. The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases. Background The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Methods Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes. Results The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases. Trial registration NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426. The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes. The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases. NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426. |
| Audience | Academic |
| Author | de Mattos, Vitoria Carneiro Pinho, João Renato Rebello Andraus, Wellington Carneiro-D'Albuquerque, Luiz Augusto Pipek, Leonardo Zumerkorn Iuamoto, Leandro Taba, João Victor Meyer, Alberto de Moura, Eduardo Guimarães Hourneaux D'Albuquerque, Eugênia Machado Carneiro Suzuki, Milena Oliveira Nascimento, Fernanda Sayuri do Setubal, João Carlos |
| AuthorAffiliation | 2 Santa Marcelina Faculty, São Paulo, São Paulo, Brazil 5 Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil 3 Colaborator, Center of Acupuncture, Department of Orthopaedics and Traumatology, University of Sao Paulo School of Medicine, São Paulo, São Paulo, Brazil 4 Department of Gastroenterology, Hospital das Clínicas, HCFMUSP, São Paulo, São Paulo, Brazil Texas A&M University, UNITED STATES 1 Faculty of Medicine FMUSP, University of São Paulo, São Paulo, São Paulo, Brazil |
| AuthorAffiliation_xml | – name: 5 Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil – name: 2 Santa Marcelina Faculty, São Paulo, São Paulo, Brazil – name: 1 Faculty of Medicine FMUSP, University of São Paulo, São Paulo, São Paulo, Brazil – name: 3 Colaborator, Center of Acupuncture, Department of Orthopaedics and Traumatology, University of Sao Paulo School of Medicine, São Paulo, São Paulo, Brazil – name: 4 Department of Gastroenterology, Hospital das Clínicas, HCFMUSP, São Paulo, São Paulo, Brazil – name: Texas A&M University, UNITED STATES |
| Author_xml | – sequence: 1 givenname: Fernanda Sayuri do surname: Nascimento fullname: Nascimento, Fernanda Sayuri do organization: Faculty of Medicine FMUSP, University of São Paulo, São Paulo, São Paulo, Brazil – sequence: 2 givenname: Milena Oliveira surname: Suzuki fullname: Suzuki, Milena Oliveira organization: Faculty of Medicine FMUSP, University of São Paulo, São Paulo, São Paulo, Brazil – sequence: 3 givenname: João Victor surname: Taba fullname: Taba, João Victor organization: Faculty of Medicine FMUSP, University of São Paulo, São Paulo, São Paulo, Brazil – sequence: 4 givenname: Vitoria Carneiro surname: de Mattos fullname: de Mattos, Vitoria Carneiro organization: Faculty of Medicine FMUSP, University of São Paulo, São Paulo, São Paulo, Brazil – sequence: 5 givenname: Leonardo Zumerkorn orcidid: 0000-0001-5268-4668 surname: Pipek fullname: Pipek, Leonardo Zumerkorn organization: Faculty of Medicine FMUSP, University of São Paulo, São Paulo, São Paulo, Brazil – sequence: 6 givenname: Eugênia Machado Carneiro surname: D'Albuquerque fullname: D'Albuquerque, Eugênia Machado Carneiro organization: Santa Marcelina Faculty, São Paulo, São Paulo, Brazil – sequence: 7 givenname: Leandro surname: Iuamoto fullname: Iuamoto, Leandro organization: Colaborator, Center of Acupuncture, Department of Orthopaedics and Traumatology, University of Sao Paulo School of Medicine, São Paulo, São Paulo, Brazil – sequence: 8 givenname: Alberto orcidid: 0000-0002-8408-0508 surname: Meyer fullname: Meyer, Alberto organization: Department of Gastroenterology, Hospital das Clínicas, HCFMUSP, São Paulo, São Paulo, Brazil – sequence: 9 givenname: Wellington surname: Andraus fullname: Andraus, Wellington organization: Department of Gastroenterology, Hospital das Clínicas, HCFMUSP, São Paulo, São Paulo, Brazil – sequence: 10 givenname: João Renato Rebello surname: Pinho fullname: Pinho, João Renato Rebello organization: Department of Gastroenterology, Hospital das Clínicas, HCFMUSP, São Paulo, São Paulo, Brazil – sequence: 11 givenname: Eduardo Guimarães Hourneaux surname: de Moura fullname: de Moura, Eduardo Guimarães Hourneaux organization: Department of Gastroenterology, Hospital das Clínicas, HCFMUSP, São Paulo, São Paulo, Brazil – sequence: 12 givenname: João Carlos surname: Setubal fullname: Setubal, João Carlos organization: Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil – sequence: 13 givenname: Luiz Augusto surname: Carneiro-D'Albuquerque fullname: Carneiro-D'Albuquerque, Luiz Augusto organization: Department of Gastroenterology, Hospital das Clínicas, HCFMUSP, São Paulo, São Paulo, Brazil |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33211762$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_1007_s00248_023_02318_3 crossref_primary_10_1016_j_clinsp_2022_100101 crossref_primary_10_3390_microorganisms10020312 |
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| Copyright | COPYRIGHT 2020 Public Library of Science 2020 Nascimento et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2020 Nascimento et al 2020 Nascimento et al |
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